Cryo-EM Facility nodes (School of Biosciences)¶
The School of Biosciences’ Cryo-Electron Microscopy Facility has purchased 3 nodes in ShARC.
that each have more than the standard number of cores for ShARC nodes (16).
Three nodes (
sharc-node138) each have:
2x Intel Xeon E5-2640 v4 processors (2.40 GHz, 10 cores per processor i.e. 20 total)
256 GB RAM (12.8 GB / CPU core)
100 Gbps Omni-Path
839 GB under
Access to the node is managed by Svet Tzokov (
email@example.com; Electron Microscopy Facility Manager).
To use the nodes you must:
Be made a member of the
cryoemGrid Engine (scheduler) Access Control List (ACL i.e. user group) by Svet Tzokov;
Submit jobs using the
cryoemGrid Engine Project;
Start interactive jobs and batch jobs in
cryoem.qGrid Engine Cluster Queue;
Running an interactive session¶
Once you have obtained permission to use the nodes you can request an interactive session on one of the nodes using:
qrshx -P cryoem -q cryoem.q
-P cryoem specifies that you want to use the
cryoem project for your session,
which gives you access to these big memory nodes and
ensures that your interactive session can run in the
cryoem.q job queue
(as can be seen if you subsequently run
qstat -u $USER from within your session).
cryoem.q job queue has a maximum job runtime (
h_rt) of 96 hours for interactive sessions (and batch jobs),
which is much greater than is standard for interactive jobs on SHARC.
Submitting batch jobs¶
Jobs can be submitted to the nodes by adding the
-P cryoem and
-q cryoem.q parameters.
For example, create a job script named
my_job_script.sh with the contents:
#!/bin/bash #$ -P cryoem #$ -q cryoem.q echo "Hello world"
You can of course add more options to the script such as a request for additional RAM
$# -l rmem=10G).
Run your script with the
You can use the
qstat command to check the status of your current job.
An output file is created in your home directory that captures your script’s outputs.
See Batch Jobs for more information on job submission and the Sun Grid Engine scheduler.